I would wait at least a week.
It takes awhile for them to purge the PNR from the system once you've completed travel. IME, when the PNR is purged (ie no longer accessible via MyItineraries, my miles post the next business day).
I assume you did all UA metal, ticketed on UA 016 card stock? It can take up to two weeks for US metal and US tickets (on UA metal) to post.
As long as your NAME and MP number on the BP matches the NAME and MP on your account the miles should post.
When boarding, do you recall watching the GA physically SCAN your BP? Most stations have the new scanner that shows the name and seat of the BP that was just scanned (in green text). I always look at that screen when the GA scans my BP. When my name shows up, I know that I'm good for miles posting.
Don't fret. You'll get your miles.
However, chances are good that if you fax in your BP's or fill out the online form, you will lose your full Y bonuses for the rebookings.
So be patient. I'd wait a week (aka 5 business days). Better to have the system do it automatically than someone at MP who might catch something else wrong with your previous MP postings.